C1GALT1C1

C1GALT1 specific chaperone 1

Basic information

Region (hg38): X:120625674-120630054

Links

ENSG00000171155 ∙ NCBI:29071 ∙ OMIM:300611 ∙ HGNC:24338 ∙ Uniprot:Q96EU7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature (Limited), mode of inheritance: XL
• hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature	XL	Allergy/Immunology/Infectious; Cardiovascular; Hematologic; Renal	The condition can involve multi-systemic manifestations, and in addition to managing cardiovascular, infectious, hematologic, and renal complications, medical management (eg, with C5 inhibitor eculizumab) has been described as beneficial	Allergy/Immunology/Infectious; Cardiovascular; Craniofacial; Hematologic; Musculoskeletal; Neurologic	36599939; 37216524

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C1GALT1C1 gene.

• Polyagglutinable_erythrocyte_syndrome (30 variants)
• not_specified (22 variants)
• Hemolytic_uremic_syndrome,_atypical,_8,_with_rhizomelic_short_stature (4 variants)
• not_provided (2 variants)
• C1GALT1C1-related_disorder (2 variants)
• Atypical_hemolytic-uremic_syndrome (1 variants)
• Abnormal_protein_O-linked_glycosylation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1GALT1C1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001011551.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	10		11
missense	3	2	44	2	2	53
nonsense	2					2
start loss	1					1
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	6	2	46	12	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1GALT1C1	protein_coding	protein_coding	ENST00000304661	1	4358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	84	115	0.730	0.00000798	2145
Missense in Polyphen		17	34.134	0.49804		672
Synonymous	0.0563	38	38.4	0.988	0.00000263	568
Loss of Function	2.32	0	6.26	0.00	4.50e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable chaperone required for the generation of 1 O- glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Probably acts as a specific molecular chaperone assisting the folding/stability of core 1 beta-3-galactosyltransferase (C1GALT1). {ECO:0000269|PubMed:12464682}.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: protein O-linked glycosylation;O-glycan processing, core 1;platelet activation;platelet morphogenesis
• Cellular component: Golgi membrane;integral component of membrane;extracellular exosome
• Molecular function: protein binding;glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity